[Biojava-l] Re: biojava-acedb

[Suman Kanuganti]

Well right, I logged in root whatsoever for the
permissions.

[root at newtondell biojava-acedb]# ant
Buildfile: build.xml

init:

prepare:
    [mkdir] Created dir:
/home/newton/biojava-acedb/ant-build

prepare-src:
    [mkdir] Created dir:
/home/newton/biojava-acedb/ant-build/src
    [mkdir] Created dir:
/home/newton/biojava-acedb/ant-build/classes
     [copy] Copying 53 files to
/home/newton/biojava-acedb/ant-build/src
     [copy] Copying 1 file to
/home/newton/biojava-acedb/ant-build/src

BUILD FAILED
file:/home/newton/biojava-acedb/build.xml:89:
/home/newton/biojava-acedb/resources not found.

-- I manually created the resources directory, then I
ant again, it tries to compile AceSequence.java at
first and fails when it is looking for
org.biojava.bio.seq.genomic.* ; I looked at api, but I
havent found this package. Even I noticed it first
time. So could you tell me how to resolve this, here
is a part of the error,

[root at newtondell biojava-acedb]# ant -buildfile
build.xml
Buildfile: build.xml

init:

prepare:

prepare-src:

compile:
    [javac] Compiling 45 source files to
/home/newton/biojava-acedb/ant-build/classes
    [javac] This version of java does not support the
classic compiler; upgrading to modern
    [javac]
/home/newton/biojava-acedb/ant-build/src/org/acedb/seq/AceSequence.java:33:
package org.biojava.bio.seq.genomic does not exist
    [javac] import org.biojava.bio.seq.genomic.*;
    [javac] ^
    [javac]
/home/newton/biojava-acedb/ant-build/src/org/acedb/seq/AceAnnotation.java:34:
org.acedb.seq.AceAnnotation should be declared
abstract; it does not define
isUnchanging(org.biojava.utils.ChangeType) in
org.acedb.seq.AceAnnotation

....... and continues, as the first one itself failed.

Thanks for any suggestions,
Suman K

--- Francois Pepin <fpepin at cs.mcgill.ca> wrote:
> Hi Suman,
> 
> My guess is that you have a permission problem
> somewhere, or that your
> disk is full or something similar.
> 
> Try to see if you can create that directory by
> yourself.
> 
> The error seems to be about being able to create the
> directory itself.
> It happened before any of the code was touched for
> compilation, so the
> problem would not be with the code, but with the
> machine that you're
> building on.
> 
> Francois
> 
> -----Original Message-----
> From: biojava-l-bounces at biojava.org
> [mailto:biojava-l-bounces at biojava.org] On Behalf Of
> Suman Kanuganti
> Sent: 10 aout, 2003 18:40
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Re: biojava-acedb
> 
> 
> I figured out something that I need to use ant to
> build the acedb-biojava, with the build.xml provided
> by the package. Now the problem:
> 
> [newton at newtondell bin]$ ant -buildfile
> ~/biojava-acedb/build.xml
> Buildfile: /home/newton/biojava-acedb/build.xml
> 
> init:
> 
> prepare:
> 
> BUILD FAILED
> file:/home/newton/biojava-acedb/build.xml:61:
> Directory /home/newton/biojava-acedb/ant-build
> creation was not successful for an unknown reason
> 
> Total time: 1 second
> 
> Any suggestions,
> Suman K
> 
> 
> --- Suman Kanuganti <bioinformatics4suman at yahoo.com>
> wrote:
> > Is there any jar for acedb-biojava for running its
> > programs. I downloaded biojava-acedb.tar but
> couldnt
> > figure how to build corresponding .jar to add it
> in
> > my
> > path.
> > 
> > Could any one tell me about this?
> > 
> > Suman K
> > 
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! SiteBuilder - Free, easy-to-use web site
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> > 
> 
> 
> =====
> Suman K
> BioInformatics Associate,
> Genomics Research,
> University of Missouri - Columbia.
> 
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> 


=====
Suman K
BioInformatics Associate,
Genomics Research,
University of Missouri - Columbia.

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